You can AMA the Quicktime files directly. If you're using a 5D Mark ii, I'd highly recommend QTChange (http://www.videotoolshed.com/product/42/qtchange) to embed timecode. If you're using the Mark iii, it will already have timecode embedded.

I still have a problem. AMA works well for me. But I must need a codec that I can't find. (And the files may have been shot with something other than a 5D.... I didn't shoot.)

It is identified as a quicktime file. Audio plays fine. Video is just a white screen. This appears to be a DVCPro file and I think I have the DVCPro codec on the machine. But all I get is a white screen.